Related Experiment Video
Updated: May 24, 2026
18:10
Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
Published on: June 16, 2011
Genetic variation and recombination in Aichi virus
Alexander N Lukashev1,2, Jan Felix Drexler2, Ilya S Belalov1
1Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia.
The Journal of General Virology
|March 2, 2012
Summary
Aichi virus (AiV) shows low genetic variability and no recombination between genotypes, suggesting reproductive isolation. Its extreme codon usage bias is driven by high cytosine content, not dinucleotide composition.
Area of Science:
- Virology
- Molecular Biology
- Genomics
Background:
- Aichi virus (AiV), a human gastroenteritis-causing kobuvirus, exhibits unique genomic features like high cytosine content and extensive RNA secondary structures.
- Previous studies highlighted AiV's distinctiveness but lacked comprehensive analysis of its full-genome genetic variability and mutational constraints.
Purpose of the Study:
- To investigate the genetic variability, recombination patterns, and mutational restrictions across the full genome of Aichi virus.
- To elucidate the origins of codon usage bias (CUB) in AiV genomes and compare them with other picornaviruses.
Main Methods:
- Sequencing of five complete coding sequences of AiV from Germany (2004), alongside analysis of five existing AiV genomes.
- Bioinformatic analysis to assess genetic variation, recombination incidence, dinucleotide frequencies (UpA, CpG), and codon usage bias (CUB).
- Application of sequence scrambling algorithms to determine the primary drivers of CUB in AiV.
Main Results:
- AiV genomes demonstrated low recombination rates and minimal synonymous/non-synonymous variation, supporting the absence of distinct serotypes.
- Absence of recombination between AiV genotypes A and B indicated reproductive isolation below the species level.
- AiV genomes strongly avoided UpA dinucleotides but showed no selection against CpG. Extreme CUB was primarily driven by high cytosine content (57%) at the third codon position, unlike other picornaviruses where dinucleotide content is a major factor.
Conclusions:
- Aichi virus exhibits remarkably low genetic diversity and distinct evolutionary constraints, including reproductive isolation between genotypes.
- The extreme codon usage bias in AiV is predominantly shaped by its high cytosine content, a unique characteristic among picornaviruses.
Related Concept Videos
00:57Viral Recombination
Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.
01:25Genetic Variation
Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles, which...
Genes exist in different versions called alleles, which...
02:53Conservative Site-specific Recombination and Phase Variation
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
The recognition sites for Cre recombinase called LoxP...
00:36Viral Mutations
A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material for adaptive...
01:09Mutation, Gene Flow, and Genetic Drift
In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
02:08Gene Conversion
Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...